The 10-year-old videogame for the Nintendo 64 games console helped usher in a new era of 3D gaming.
It is also one of only five games ever to receive a 10 out of 10 review score from Edge magazine.
Five of the top 10 titles were made only for Nintendo machines, including Super Mario 64, in third spot.
The full list of 100 titles has been compiled for a special edition of Edge magazine.
Tony Mott, editor-in-chief of Edge, said: "If you were new to video games and were going to go out and buy 100 games to make an instant collection, then these would be the games to buy."
He added: "Ocarina of Time is nearly 10 years old, but its position at the top slot in Edge's 100 Best Videogames shows that great game design does not age.
"In visual terms, it obviously cannot compete with today's Xbox 360 and PS3 productions, but, as with many classics, its appeal is about so much more than its appearance."
Only one PC game makes the top 10 - classic first person shooter Half Life 2. Microsoft's Xbox also has only one representative in the elite list - with Halo: Combat Evolved at number seven.
Only five games for the next generation of consoles have made the top 100 - Pro Evolution Soccer 6, at number 15, Oblivion, at number 19, Virtua Fighter 5, in 38th spot, Virtua Tennis 3 at number 80, and Crackdown at 100.
Tony Mott said: "Crackdown hasn't been around long but has proved itself to be a very good game. It will be interesting to see people's reaction to that.
"If we did this poll in five year's time, I would hope to see more PS3 and Xbox 360 games in the list. But I don't think anyone would argue we have seen that many classics in this new generation."
The list was drawn together in three stages - thousands of reader votes, combined with expert opinion in the games industry and finally input from Edge's own editorial team.
Mr Mott said Ocarina of Time was the reader favourite as well as the overall winner.
'Brilliantly well'
He said: "It appeared not long after games made the shift to 3D; everyone was wondering if it could make the transition.
"It was a very ambitious game. The way they were able to engineer it in a 3D context was a success; it worked brilliantly well."
But he said the intention behind the poll was not to create a "nostalgia festival".
"These games had to stand up today. People will be surprised by the small amount of very old games that have made it through.
"Often these types of lists are full of games like Space Invaders and Pong - which we recognise as classics, as important games - but they don't necessarily stand up to play today."
He added: "I love the fact that old games are being made available to audiences via Xbox Live, PlayStation Network and through compilations but I am not convinced that younger players will play them and appreciate them in the way we did the first time round.
"It's very hard for younger players who play something graphically-rich like Gears of War to then play something like Robotron.
"I think it will be for the greater good of the industry when more effort is put into the content of games than the way it is presented visually."
The five titles to have received a maximum review score from Edge are: Zelda: Ocarina of Time, Half-Life 2, Gran Turismo, Super Mario 64 and Halo.